Change permalinks for posts but not for custom post types

When you register your post type, the with_front argument of rewrite should be false, so the permastruct is not appended to the front of your custom post type permalink.

$args = array(
    // snip...
    'rewrite' => array( 'with_front' => false ),
    // snip...
); 

register_post_type( 'your-post-type', $args );